I agree about the Quad, But the SCT,Diablo,etc are flash tuners. They remove the factory tune and save it and replace it with there tune or a custom, where the Quad. goes between the factory computer and the engine and intersepts the the signals and changes them.The Quad does not change any thing in the factory computer, it modifies the signals comming from it. Any programer that plugs into the OBDII port and removes/changes the factory program then you unplug it could possibly leave a fragment of the moified tune behind when its changed back to the factory tune.I have had flash tuners before and know how they work. The Quad Adrenalin works between the factory computer and the engine, It does not change or remove the factory tune. And since it dosn't modify the factory program it leaves no footprint. I don't have to change back to the factory program to take it to a Ford Dealer, I just unplug the main wire. Think about it be for you respond next time. Why do you have to save the factory program

 

To make this as simple as I know to explain this, we are talking about three different components:
PCM=Powertrain Control Module or ECM=Engine Control Module-This is the "computer"
TCM=Transmission Control Module
FICM=Fuel Injector Control Module

The SCT reprograms the PCM and the TCM. It does not do anything to the FICM itself, it changes the information that the PCM sends to the FICM which is about the same as the Quad does between the PCM and FICM. There is no way the SCT can burn anything into the FICM. The FICM fails because the solder on the circuit board cracks and falls off, this can happen stock or with any given tuner or programmer. The wire harness also chaffes and shorts out. The FICM is tested by checking voltage output. The FICM can be reworked to increase the voltage output and it can be reprogrammed, however for now it must be removed from the vehicle and sent out to be done then put back in the truck. Alot of guy with newer stratagies are getting the "rollback" which gives you a earlier stratagy for better mileage and power.
The basic difference between the SCT and any of the other boxed tuners or programmers is the SCT has its tunes written for the stratagy on your truck where the others are shall we say "generic". That is why you can't just put my SCT on your truck but you can switch the others. The big difference is the SCT tunes the transmission and the custom tunes are written for your truck and your setup, if you have studs or not, if you go to bigger injectors or a bigger turbo or twins, if you add nitrous or water/meth. its just a matter of updating your tune.
As far as a footprint goes, when the tech does a diagnostic he will see what looks like the batteries were disconnected. He will have be very good and look really deep to find anything more. More often than not they see the aftermarket exhaust, the aftermarket air filter or a bunch of guages and make an assumption that you are running some kind of programmer. What they say and what they can prove are not the same. I've heard of dealers that will dig their heels over any mod weather its related or not, there are also dealers that don't care if your programmer of choice is in plain view and hooked up.
I hope I havn't left anything out or misstated and confused things, if anyone can explain this better please do.